Class PDBStrand

All Implemented Interfaces:
Serializable, Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IStrand

public class PDBStrand extends Strand
An entry in the PDB database. It is not just a regular protein, but the regular PDB mix of protein or protein complexes, ligands, water molecules and other species.
Author:
Egon Willighagen
See Also:
Source code:
main
Belongs to CDK module:
pdb
Keywords:
polymer
Created on:
2006-04-19
  • Constructor Details

    • PDBStrand

      public PDBStrand()
      Constructs a new Polymer to store the Monomers.
  • Method Details

    • addAtom

      public void addAtom(IAtom oAtom, IMonomer oMonomer)
      Adds the atom oAtom to a specified Monomer. Additionally, it keeps record of the iCode.
      Specified by:
      addAtom in interface IStrand
      Overrides:
      addAtom in class Strand
      Parameters:
      oAtom - The atom to add
      oMonomer - The monomer the atom belongs to
    • getMonomerNamesInSequentialOrder

      public Collection<String> getMonomerNamesInSequentialOrder()
      Returns the monomer names in the order in which they were added.
      See Also:
    • toString

      public String toString()
      Description copied from class: AtomContainer
      Returns a one line description of this IChemObject.
      Specified by:
      toString in interface IChemObject
      Overrides:
      toString in class Strand
      Returns:
      a String representation of this object